Understanding the Psychophysiological Mechanisms Underlying Context-Dependent Gains and Losses Among Smokers

https://openworks.mdanderson.org/sumexp21/1181/thumbnail.jp

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. CONCLUSIONS: VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion

Implementation of a Comprehensive Tobacco Free Workplace Program in Agencies Serving the Homeless and Vulnerably Housed

Although there have been substantial decreases in the prevalence of cigarette smoking in the last two decades, these overall population estimates often fail to account for subpopulations, such as individuals who are homeless or vulnerably housed, that have disproportionately high smoking rates. Despite this, clinicians do not commonly address tobacco use among individuals who are homeless. Tobacco-free workplace programs, like TTTF, are evidence-based, tobacco control initiatives that may be effective in increasing capacity to address tobacco use within homeless-serving community agencies by addressing known clinician barriers to intervention by providing education, specialized training, and resources to promote and assist quit attempts. Here, we examine the outcomes of TTTF’s implementation within 4 agencies that provide housing or other services to individuals who are homeless or vulnerably housed. Pre- and post-implementation data were collected from clinicians (N=68) to assess changes in training receipt, knowledge, and intervention behaviors. Results indicated significant gains in clinicians’ receipt of training in 9 (of 9) target areas (ps≤0.0042) and a 53% knowledge gain (ps<0.0001). From pre- to post-implementation, there were mean increases in the use of the 5A’s (ask, advise, assess, assist, and arrange) and other evidence-based interventions for tobacco cessation, with significant gains seen over time in assisting residents/clients to quit, arranging follow-ups, and providing or referring for non-nicotine medications (ps≤0.0491). Overall, TTTF improved clinicians’ capacity to address tobacco use among homeless and vulnerably housed individuals and may serve as a model for tobacco control efforts in similar agencies. This project was completed with contributions from Bryce Kyburz, Teresa Williams, and Kathleen Casey from Integral Care at Austin.Health and Human Performance, Department ofHonors Colleg

Clinician Training in the Adaptation of a Comprehensive Tobacco-Free Workplace Program in Agencies Serving the Homeless and Vulnerably Housed

Tobacco use is exceedingly high among those who are homeless or at risk of homelessness but not commonly addressed by clinicians. Taking Texas Tobacco Free (TTTF) is a tobacco control program that addresses known clinician barriers to intervention (e.g., low training receipt, limited resources). Here, we examine the process and outcomes of TTTF&rsquo;s adaptation within four agencies that provide housing or other services to individuals who are homeless or vulnerably housed. Pre- and post-implementation data were collected from clinicians (N = 68) to assess changes in training receipt, knowledge, and intervention behaviors, relative to program goals. Results indicated significant gains in clinicians&rsquo; receipt of training in 9 (of 9) target areas (p&rsquo;s &le; 0.0042) and a 53% knowledge gain (p &lt; 0.0001). From pre- to post-implementation, there were mean increases in the use of the 5As (ask, advise, assess, assist, and arrange) and other evidence-based interventions for tobacco cessation, with significant gains seen in assisting residents/clients to quit, arranging follow-ups, and providing or referring for non-nicotine medications (p&rsquo;s &le; 0.0491). All program goals, except gains related to advising smokers to quit and the use of specific interventions (behavioral counseling), were met. Overall, TTTF improved clinicians&rsquo; capacity to address tobacco use among homeless and vulnerably housed individuals and can serve as a model for tobacco control efforts in similar agencies

Quality of life of patients with oesophageal cancer in Taiwan: validation and application of the Taiwan Chinese (Mandarin) version of the EORTC QLQ-OES18: a brief communication

[[abstract]]Purpose: The aim of this study was to examine the reliability and validity, and the application of the Taiwan Chinese Version of the EORTC QLQ-OES18. Methods: The authors translated the questionnaire according to the guideline of the EORTC. Ninety-five patients with oesophageal cancer in National Taiwan University Hospital were interviewed using the questionnaire and the EORTC QLQ-C30 between October 2002 and September 2007. Answer distribution and psychometric properties of the EORTC QLQ-OES18 were examined. Results: The mean age of the patients was 60?years (SD 12?years). Most of the patients were in advanced stages of disease, with two-thirds off-treatment. The Cronbach's alpha coefficients were satisfactory (0.77-0.82) or near-satisfactory (pain: 0.67). The item-to-own and item-to-other scale correlations showed satisfactory results. Patients who were on-treatment versus off-treatment had significantly poorer quality of life scores in dysphagia, dry mouth, and taste, and a borderline poorer score in cough. Opposite situations were seen in the scales of reflux and choking. Conclusions: The EORTC QLQ-OES18 is a valid instrument to assess quality of life issues in patients with oesophageal cancer in Taiwan

Additional file 8: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Figure S3. VIPER was run on a dataset (12 samples; single end data; 36.7 M reads on average) and finished in 24 h. VIPER performance during this run is captured using Ganglia on a 96GB RAM 6 processor Intel Xeon machine. (a) System usage and (b) CPU load captured showing how VIPER is parallelized across 6 processors with (c) ~35G memory utilized for the alignment part of the pipeline. (PDF 79 kb

Additional file 4: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Figure S1. Graphical overview of the computational steps performed by VIPER processing a single fastq file. The nodes of the graph represent the execution of a rule and a directed edge between node A and B means that the rule underlying node B needs the output of node A as an input. A path in the graph represents a sequence of jobs that have to be executed serially, but disjoint paths can be run in parallel. This specific directed acyclic graph (DAG) was automatically generated by VIPER based on the directive to run the rule named ‘target’, using a single fastq file as input. (PDF 436 kb

Additional file 1: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Config Example (YAML 6 kb

Additional file 1: of VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Config Example (YAML 6 kb